User blog:Fuse809/Creating molecular structures using free software
If you ever need to draw structures of drugs or other molecules I recommend MarvinSketch '''and/or ACD/ChemSketch' (both of which are available for non-commercial use for free and can produce 3D structures too it's just they're rather non-customizable) for '''2D structures' and Accelrys DS Visualizer,' Avogadro',' Jmol '''and/or' QuteMol' (all four of which are available for free) for '''3D models'. 2D structural editors ACD/ChemSketch ACD/ChemSketch can only export to traditional image formats (BMP, EMF, GIF, JPG, PCX, PNG, TIF, WMF) and not to scaled vector graphics (SVGs). WMF files can be converted to SVG files using Scribus which is also available for free, but of course this adds to the time one spends creating these structures. ACD/ChemSketch only works on Windows operating systems. MarvinSketch .]] '''MarvinSketch can export to just about every format and is far more customizable when it comes to the structures it produces. For example, the different''' elements''' (or more specifically their labels) can be coloured CPK'Which is a popular colouring scheme for chemical elements especially for use in colouring 3D models, carbon is grey/black, hydrogen is white, oxygen is red, nitrogen is blue, ''etc. This http://jmol.sourceforge.net/jscolors/ is a fairly comprehensive list of the different colour assignments for the various elements. or '''monochrome (i.e., in black and white). MarvinSketch can also perform various different calculations'''Such as of elemental composition, molecular weight, % composition for the various elements contained therein, also of partition coefficients, pKas, water solubility, different stereoisomers and cis/trans-isomers, molecular surface area (i.e., due to van der waals interactions), polar surface area and others for free, display stereocentres, determine the IUPAC name for a given structure, import structures from their common/IUPAC names,for which the keyboard shortcut is '''Ctrl+Shift+N, FYI display chemical reaction equations, plus one can choose if carbon labels are shown or not and one can customize the size of element labels (like O for oxygen, F for fluorine, Cl for chlorine, etc.). MarvinSketch can also export structures to various different molecular formats (like MOL, SDF, PDB, XYZ, MRV, etc.) and can run on any operating system (as it is powered by Java which is cross-platform). 3D structural editors Static structures Amongst the 3D structure editors I mentioned Accelrys and Avogadro can only do static models which they can also do only in traditional image formats. Accelrys is generally my favourite but it is only legally available for non-commercial use,Part of the reason for my preference is that its colours are far more customizable, plus it can display aromatic rings as delocalized systems unlike Avogadro which as far as I am aware of can only show aromatic rings with double bonds. whereas Avogadro is completely free for whatever purpose you wish to use it. Technically Accelrys can also do 2D structures but I have found them very difficult to customize, granted I haven't had much experience with Accelrys as I've only used it for less than a week. Accelrys can run on Linux and Windows whereas Avogadro can run on Mac OS X, Linux and Windows. Animated structures in GIF format QuteMol and Jmol can do animated structures in GIF format, but both have their limitations. QuteMol can't represent double bonds and rather represents them as single bonds, plus it hasn't been updated since 2007 and has a few bugs (for me it sometimes gets the colour of the chemical elements wrong), but it can export structures straight to animated GIF format which can be a timesaver. It can run only on Windows and Mac OS X. Jmol can't do animated GIF structures itself, or at least it can't do them well, but it can be programmed (via its script editor) to capture serial images (or frames) in PNG format at a different angles each timeAlthough the differences between the angle, in terms of degrees, is kept constant until a complete 360 degree revolution is complete. Then these PNG images can be converted, using GNU Image Manipulation Program (GIMP), to an animated GIF file. Usually I use 60 frames spaced 6 degrees apart. The Jmol code I use for the formation of these serial images taken at different angles is: name = "./Work0000.png"; nFrames = 60; nDegrees = 6; thisFrame = 0; width = 539; height = 260; message loop; thisFrame = thisFrame + 1; fileName = name.replace("0000","" + ("0000" + thisFrame)-40); rotate y @ndegrees; frame next; # only use this if you have a multiframe file. refresh; write image @width @height @fileName; if (thisFrame < nFrames);goto loop;endif; Where''' nFrames''' is the parameter that determines the number of frames used, nDegrees is the angle between each PNG image that is captured, width is the width of the PNG images, height is the height of the PNG images and the work parameter is where these captured PNG images are stored. Notes Category:Blog posts